Sudan's president, Omar al-Bashir, is in Chad on his first visit to a member state of the International Criminal Court, which last week issued a second warrant for his arrest on charges of genocide. Member states are legally obliged to arrest fugitives on their soil but Chad has refused.

Bashir arrived in N'djamena yesterday evening to attend a meeting of leaders of the Community of Sahel-Saharan States that is being held today.

Since the ICC first issued a warrant for his arrest in March 2009 for alleged war crimes in Darfur, Bashir has drastically cut his international travel, only visiting nearby states that have not signed up to the Hague-based court.

Ahead of the meeting, international human rights groups had called on Chad, which borders Sudan, to arrest Bashir. But this was always going to be unlikely, given the complicated history between the countries – and indeed their mutual role in the Darfur conflict.

Bashir was met at the airport in the Chadian capital by President Idriss Deby, and given a symbolic key to the city.

"We are not obliged to arrest Omar Hassan al-Bashir," Ahmat Mahamat Bachir, Chad's interior and security minister, told Reuters. "Bashir is a sitting president. I have never seen a sitting president arrested on his travels by the host country."

Chad's decision highlights the difficulty faced by the ICC in bringing Bashir to trial. All the court's arrest warrants to date – relating to Uganda, Central African Republic and Democratic Republic of Congo and Sudan – concern Africa, which has led to a perception in some parts of the continent that it is being unfairly targeted. The African Union itself has urged its members not to arrest Bashir.

But the ICC points out that in the first three cases the respective African governments requested its intervention, and only with Sudan, which is not a member of the court, was the matter referred by the UN Security Council. Yesterday a court spokesman stressed that, as a member state, Chad was under a legal obligation to arrest Bashir.

In recent years relations between the two countries have been extremely tense, with each sponsoring proxy militias operating in and alongside Darfur to destabilise the other. But in February Bashir and Deby agreed to stop supporting the cross-border rebel groups. Relations have since thawed considerably, and Deby, whose own human rights record is very poor, has since visited Khartoum.

"Chad and Sudan had a problem in the past," Bashir told reporters when he arrived in N'djamena. "Now this problem is solved. We are brothers."

It could be argued that Chad might have risked conflict with Sudan had it arrested Bashir. But human groups said this was no excuse for welcoming him to the country.

"A political deal between Chad and Sudan is no justification for shielding alleged war criminals," said Elise Keppler, of Human Rights Watch's international justice program. "Instead of protecting a fugitive from justice, Chad should urge Sudan to cooperate with the ICC."

Bashir was initially charged in 2009 with war crimes and crimes against humanity over his role in Darfur, where his government began a brutal counter-insurgency operation in 2003.

On 12 July, a second arrest warrant was issued to include genocide charges related to campaigns targeting the Fur, Masalit and Zaghawa ethnic groups there. The ICC has also issued arrest warrants for a Sudanese government minister, a pro-government militia leader, and three Darfuri rebel leaders.